Characterization of the genetic determinants of context-specific DNA methylation in primary monocytes.

To better understand inter-individual variation in sensitivity of DNA methylation (DNAm) to immune activity, we characterized effects of inflammatory stimuli on primary monocyte DNAm (n = 190). We find that monocyte DNAm is site-dependently sensitive to lipopolysaccharide (LPS), with LPS-induced demethylation occurring following hydroxymethylation. We identify 7,359 high-confidence immune-modulated CpGs (imCpGs) that differ in genomic localization and transcription factor usage according to whether they represent a gain or loss in DNAm. Demethylated imCpGs are profoundly enriched for enhancers and colocalize to genes enriched for disease associations, especially cancer. DNAm is age associated, and we find that 24-h LPS exposure triggers approximately 6 months of gain in epigenetic age, directly linking epigenetic aging with innate immune activity. By integrating LPS-induced changes in DNAm with genetic variation, we identify 234 imCpGs under local genetic control. Exploring shared causal loci between LPS-induced DNAm responses and human disease traits highlights examples of disease-associated loci that modulate imCpG formation.

Monkeypox Virus Detection in Different Clinical Specimen Types.

A global monkeypox outbreak began in May 2022. Limited data exist on specimen type performance in associated molecular diagnostics. Consequently, a diverse range of specimen sources were collected in the initial weeks of the outbreak in Ontario, Canada. Our clinical evaluation identified skin lesions as the optimal diagnostic specimen source.

Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity.

Natural Killer cells are innate lymphocytes with central roles in immunosurveillance and are implicated in autoimmune pathogenesis. The degree to which regulatory variants affect Natural Killer cell gene expression is poorly understood. Here we perform expression quantitative trait locus mapping of negatively selected Natural Killer cells from a population of healthy Europeans (n = 245). We find a significant subset of genes demonstrate expression quantitative trait loci specific to Natural Killer cells and these are highly informative of human disease, in particular autoimmunity. A Natural Killer cell transcriptome-wide association study across five common autoimmune diseases identifies further novel associations at 27 genes. In addition to these cis observations, we find novel master-regulatory regions impacting expression of trans gene networks at regions including 19q13.4, the Killer cell Immunoglobulin-like Receptor region, GNLY, MC1R and UVSSA. Our findings provide new insights into the unique biology of Natural Killer cells, demonstrating markedly different expression quantitative trait loci from other immune cells, with implications for disease mechanisms.

Fine-Scale Genetic Structure in the United Arab Emirates Reflects Endogamous and Consanguineous Culture, Population History, and Geography.

The indigenous population of the United Arab Emirates (UAE) has a unique demographic and cultural history. Its tradition of endogamy and consanguinity is expected to produce genetic homogeneity and partitioning of gene pools while population movements and intercontinental trade are likely to have contributed to genetic diversity. Emiratis and neighboring populations of the Middle East have been underrepresented in the population genetics literature with few studies covering the broader genetic history of the Arabian Peninsula. Here, we genotyped 1,198 individuals from the seven Emirates using 1.7 million markers and by employing haplotype-based algorithms and admixture analyses, we reveal the fine-scale genetic structure of the Emirati population. Shared ancestry and gene flow with neighboring populations display their unique geographic position while increased intra- versus inter-Emirati kinship and sharing of uniparental haplogroups, reflect the endogamous and consanguineous cultural traditions of the Emirates and their tribes.

Context-specific regulation of surface and soluble IL7R expression by an autoimmune risk allele.

IL-7 is a key factor in T cell immunity and common variants at IL7R, encoding its receptor, are associated with autoimmune disease susceptibility. IL7R mRNA is induced in stimulated monocytes, yet a function for IL7R in monocyte biology remains unexplored. Here we characterize genetic regulation of IL7R at the protein level in healthy individuals, and find that monocyte surface and soluble IL7R (sIL7R) are markedly induced by lipopolysaccharide. In monocytes, both surface IL7R and sIL7R expression strongly associate with allelic carriage of rs6897932, a disease-associated IL7R polymorphism. Monocytes produce more sIL7R than CD4 + T cells, and the amount is additionally correlated with the expression of DDX39A, encoding a splicing factor. Synovial fluid-derived monocytes from patients with spondyloarthritis are enriched for IL7R+ cells with a unique transcriptional profile that overlaps with IL-7-induced gene sets. Our data thus suggest a previously unappreciated function for monocytes in IL-7 biology and IL7R-associated diseases.

Perspective: Potential Impact and Therapeutic Implications of Oncogenic PI3K Activation on Chromosomal Instability.

Genetic activation of the class I PI3K pathway is very common in cancer. This mostly results from oncogenic mutations in PIK3CA, the gene encoding the ubiquitously expressed PI3Kα catalytic subunit, or from inactivation of the PTEN tumour suppressor, a lipid phosphatase that opposes class I PI3K signalling. The clinical impact of PI3K inhibitors in solid tumours, aimed at dampening cancer-cell-intrinsic PI3K activity, has thus far been limited. Challenges include poor drug tolerance, incomplete pathway inhibition and pre-existing or inhibitor-induced resistance. The principle of pharmacologically targeting cancer-cell-intrinsic PI3K activity also assumes that all cancer-promoting effects of PI3K activation are reversible, which might not be the case. Emerging evidence suggests that genetic PI3K pathway activation can induce and/or allow cells to tolerate chromosomal instability, which-even if occurring in a low fraction of the cell population-might help to facilitate and/or drive tumour evolution. While it is clear that such genomic events cannot be reverted pharmacologically, a role for PI3K in the regulation of chromosomal instability could be exploited by using PI3K pathway inhibitors to prevent those genomic events from happening and/or reduce the pace at which they are occurring, thereby dampening cancer development or progression. Such an impact might be most effective in tumours with clonal PI3K activation and achievable at lower drug doses than the maximum-tolerated doses of PI3K inhibitors currently used in the clinic.

Genomic Response to Vitamin D Supplementation in the Setting of a Randomized, Placebo-Controlled Trial.

BACKGROUND: Vitamin D deficiency has been associated with multiple diseases, but the causal relevance and underlying processes are not fully understood. Elucidating the mechanisms of action of drug treatments in humans is challenging, but application of functional genomic approaches in randomized trials may afford an opportunity to systematically assess molecular responses. METHODS: In the Biochemical Efficacy and Safety Trial of Vitamin D (BEST-D), a double-blind, placebo-controlled, dose-finding, randomized clinical trial, 305 community-dwelling individuals aged over 65 years were randomly allocated to treatment with vitamin D3 4000 IU, 2000 IU or placebo daily for 12 months. Genome-wide genotypes at baseline, and transcriptome and plasma levels of cytokines (IFN-γ, IL-10, IL-8, IL-6 and TNF-α) at baseline and after 12 months, were measured. The trial had >90% power to detect 1.2-fold changes in gene expression. FINDINGS: Allocation to vitamin D for 12-months was associated with 2-fold higher plasma levels of 25-hydroxy-vitamin D (25[OH]D, 4000 IU regimen), but had no significant effect on whole-blood gene expression (FDR < 5%) or on plasma levels of cytokines compared with placebo. In pre-specified analysis, rs7041 (intron variant, GC) had a significant effect on circulating levels of 25(OH)D in the low dose, but not in the placebo or high dose vitamin D regimen. A gene expression quantitative trait locus analysis (eQTL) demonstrated evidence of 31,568 cis-eQTLs (unique SNP-probe pairs) among individuals at baseline and 34,254 after supplementation for 12 months (any dose). No significant associations involving vitamin D supplementation response eQTLs were found. INTERPRETATION: We performed a comprehensive functional genomics and molecular analysis of vitamin D supplementation in a randomized, placebo-controlled trial. Although this study was limited to mostly Caucasian individuals aged over 65 years, the results differ from many previous studies and do not support a strong effect of vitamin D on long-term transcriptomic changes in blood or on plasma cytokine levels. The trial demonstrates the feasibility of applying functional genomic and genetic approaches in randomized trials to assess molecular and individual level responses. KEY RESULT: Supplementation with high-dose vitamin D in older people for 12 months in a randomized, placebo-controlled trial had no significant effect on gene expression or on plasma concentrations of selected cytokines. TRIAL REGISTRATION: SRCTN registry (Number 07034656) and the European Clinical Trials Database (EudraCT Number 2011-005763-24).

Oncogenic PIK3CA induces centrosome amplification and tolerance to genome doubling.

Mutations in PIK3CA are very frequent in cancer and lead to sustained PI3K pathway activation. The impact of acute expression of mutant PIK3CA during early stages of malignancy is unknown. Using a mouse model to activate the Pik3ca H1047R hotspot mutation in the heterozygous state from its endogenous locus, we here report that mutant Pik3ca induces centrosome amplification in cultured cells (through a pathway involving AKT, ROCK and CDK2/Cyclin E-nucleophosmin) and in mouse tissues, and increased in vitro cellular tolerance to spontaneous genome doubling. We also present evidence that the majority of PIK3CA H1047R mutations in the TCGA breast cancer cohort precede genome doubling. These previously unappreciated roles of PIK3CA mutation show that PI3K signalling can contribute to the generation of irreversible genomic changes in cancer. While this can limit the impact of PI3K-targeted therapies, these findings also open the opportunity for therapeutic approaches aimed at limiting tumour heterogeneity and evolution.

No influence of carbonation on glycemic response, gastric emptying, and satiety of sweetened drinks.

OBJECTIVE: The aim of this study was to examine the effect of carbonation of sweetened beverages on glycemic response, gastric emptying, and satiety. METHODS: After an overnight fast, 15 healthy individuals (6 women, 9 men) consumed a 500 mL beverage containing 50 g glucose that was noncarbonated (NC), low carbonated (LC), or high carbonated (HC) at a standardized rate of consumption (100 mL/min). Blood glucose was measured at baseline and at 15, 30, 45, 60, 90, and 120 min after beverage consumption. Antral cross-sectional area was measured using ultrasound at baseline, 5, 10, 20, 30, 40, 50, 60, 90, and 120 min; for the estimation of gastric volume and gastric emptying rate. Satiety was assessed using electronic visual analog scales at the same time points as the blood glucose measurement. RESULTS: There were no significant differences in glycemic response among the test beverages. Higher carbonation levels significantly increased antral cross-sectional area during the first 20 min after beverage consumption (P < 0.010) but did not translate into significant differences in gastric volume or gastric emptying rates. There was no significant effect of carbonation on satiety, but the area under the curve for thirst was significantly lower for HC compared with NC (P = 0.009). CONCLUSIONS: The carbonation of a simple glucose solution did not increase glycemic response nor alter gastric emptying and subjective feelings of satiety (with the exception of thirst). The present study suggests that carbonation does not alter glycemic response.

Physical Form of Dietary Fat Alters Postprandial Substrate Utilization and Glycemic Response in Healthy Chinese Men.

Background: Dietary fats elicit various physiological responses, with the physical form of fat reported to alter fat digestion and absorption.Objectives: The primary aims were to compare the effects of dietary fat in 2 physical forms (liquid and oleogel) and 2 degrees of saturation (saturated and polyunsaturated) on postprandial energy expenditure (EE) and substrate oxidation, glycemia, and appetite.Methods: The study was a randomized, controlled crossover trial. Sixteen normal-weight, healthy Chinese men completed the study [mean ± SD age: 28 ± 6 y; body mass index (in kg/m2): 22.9 ± 3.1]. After an overnight fast, participants had their body weight measured and entered an indirect whole-room calorimeter (WRC). After baseline measurements, participants consumed orange juice and rice porridge alone (control), with 22.25 g coconut oil or sunflower oil or with 25 g coconut oleogel or sunflower oleogel in random order with a 5-d washout period between treatments. EE, substrate oxidation, capillary blood glucose, and appetite were measured over 195 min in a WRC. Participants completed a meal challenge to assess appetite. Test meals effects were compared by using repeated-measures ANOVA.Results: Fat saturation did not affect all study outcomes significantly. When data were pooled based on the physical form of dietary fat, EE did not differ. However, significantly higher carbohydrate oxidation (P = 0.03) and a trend of lower fat oxidation (P = 0.07) were found after the liquid oil than after the oleogel or control treatments. Postprandial capillary glucose was also significantly lower after the liquid oil than after the oleogel or control treatments (P < 0.001). Appetite was not affected by the physical form and the saturation of dietary fats.Conclusions: The saturation of dietary fat did not affect postprandial glucose, EE, substrate oxidation, or appetite. However, oleogel prevented the glycemic-lowering and fat-oxidation effects induced by liquid oil in Chinese men. Future work on oleogel should focus on cardiometabolic risk factors. This study was registered at clinicaltrials.gov as NCT02702726.

Effect of fat type in baked bread on amylose-lipid complex formation and glycaemic response.

The formation of amylose-lipid complexes (ALC) had been associated with reduced starch digestibility. A few studies have directly characterised the extent of ALC formation with glycaemic response. The objectives of this study were to investigate the effect of using fats with varying degree of saturation and chain length on ALC formation as well as glycaemic and insulinaemic responses after consumption of bread. Healthy men consumed five test breads in a random order: control bread without any added fats (CTR) and breads baked with butter (BTR), coconut oil (COC), grapeseed oil (GRP) or olive oil (OLV). There was a significant difference in glycaemic response between the different test breads (P=0·002), primarily due to COC having a lower response than CTR (P=0·016), but no significant differences between fat types were observed. Insulinaemic response was not altered by the addition of fats/oils. Although BTR was more insulinotropic than GRP (P<0·05), postprandial ß-cell function did not differ significantly. The complexing index (CI), a measure of ALC formation, was significantly higher for COC and OLV compared with BTR and GRP (P<0·05). CI was significantly negatively correlated with incremental AUC (IAUC) of change in blood glucose concentrations over time (IAUCglucose) (r -0·365, P=0·001). Linear regression analysis showed that CI explained 13·3 % of the variance and was a significant predictor of IAUCglucose (ß=-1·265, P=0·001), but IAUCinsulin did not predict IAUCglucose. Our study indicated that a simple way to modulate glycaemic response in bread could lie in the choice of fats/oils, with coconut oil showing the greatest attenuation of glycaemic response.

Rapid estimation of the energy content of composite foods: the application of the Calorie Answer™.

The estimation of calories in foods is central in the maintenance of body weight and energy regulation. Conventional laboratory analysis using bomb calorimetry to determine calorie content is expensive and time-consuming. There is a need to explore alternative techniques for calorie estimation that requires less processing and resources. The potential of using near infrared spectroscopy for calorie measurements with Calorie Answer™ was evaluated in this study. The caloric content of 105 different foods was measured, and compared against values reported on nutrition labels. The average percentage relative standard deviation for triplicate measurements was 1.7% for all foods. The percentage difference between stated and measured calories was modest, at 4.0% for all foods. Stated and measured calorie contents were significantly and highly correlated (R2=0.98, p<0.001). The use of near infrared spectroscopy, using Calorie Answer™, is a rapid, reproducible and cost-effective way of measuring calorie content in a diverse range of foods. Its application in many parts of Asia Pacific and other emerging nations will generate much needed information on the calorie content of complex foods consumed by people living in these regions.

Mineral decline due to modernization of food habits.

Calcium and other micronutrients are essential for health and well-being. Dairy products are the main sources of calcium in western countries. In most regions of Asia, the consumption of these products is limited due to the lactose intolerance and costs. A major contributor to the micronutrients intake in this region is the consumption of small fish, such as anchovies. Traditionally, dried anchovies are consumed as a whole body. Recently, an increasingly popular method of eating anchovies has been to eat it in a cleaned, eviscerated form. This brief communication highlights how "modernization" of food habits may have unintentional nutritional consequences. A minor change in the dietary habits of eating cleaned anchovies may lead to a reduction in micronutrients intake. This reinforces the need for caution when we modernize our traditional eating habits.

Can bread processing conditions alter glycaemic response?

Bread is a staple food that is traditionally made from wheat flour. This study aimed to compare the starch digestibility of western baked bread and oriental steamed bread. Four types of bread were prepared: western baked bread (WBB) and oriental steamed bread (OSB), modified baked bread (MBB) made with the OSB recipe and WBB processing, and modified steamed bread (MSB) made with the WBB recipe and OSB processing. MBB showed the highest starch digestibility in vitro, followed by WBB, OSB and MSB. A similar trend was observed for glycaemic response in vivo. MBB, WBB, OSB and MSB had a glycaemic index of 75±4, 71±5, 68±5 and 65±4, respectively. Processing differences had a more pronounced effect on starch digestibility in bread, and steamed bread was healthier in terms of glycaemic response. The manipulation of processing conditions could be an innovative route to alter the glycaemic response of carbohydrate-rich foods.

Genomic mapping of the MHC transactivator CIITA using an integrated ChIP-seq and genetical genomics approach.

BACKGROUND: The master transactivator CIITA is essential to the regulation of Major Histocompatibility Complex (MHC)class II genes and an effective immune response. CIITA is known to modulate a small number of non-MHC genes involved in antigen presentation such as CD74 and B2M but its broader genome-wide function and relationship with underlying genetic diversity has not been resolved. RESULTS: We report the first genome-wide ChIP-seq map for CIITA and complement this by mapping inter-individual variation in CIITA expression as a quantitative trait. We analyse CIITA recruitment for pathophysiologically relevant primary human B cells and monocytes, resting and treated with interferon-gamma, in the context of the epigenomic regulatory landscape and DNA-binding proteins associated with the CIITA enhanceosome including RFX, CREB1/ATF1 and NFY. We confirm recruitment to proximal promoter sequences in MHC class II genes and more distally involving the canonical CIITA enhanceosome. Overall, we map 843 CIITA binding intervals involving 442 genes and find 95% of intervals are located outside the MHC and 60% not associated with RFX5 binding. Binding intervals are enriched for genes involved in immune function n and infectious disease with novel loci including major histone gene clusters. Were solve differentially expressed genes associated in trans with a CIITA intronic sequence variant, integrate with CIITA recruitment and show how this is mediated by allele-specific recruitment of NF-kB. CONCLUSIONS: Our results indicate a broader role for CIITA beyond the MHC involving immune-related genes.We provide new insights into allele-specific regulation of CIITA informative for understanding gene function and disease.

Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression.

To systematically investigate the impact of immune stimulation upon regulatory variant activity, we exposed primary monocytes from 432 healthy Europeans to interferon-γ (IFN-γ) or differing durations of lipopolysaccharide and mapped expression quantitative trait loci (eQTLs). More than half of cis-eQTLs identified, involving hundreds of genes and associated pathways, are detected specifically in stimulated monocytes. Induced innate immune activity reveals multiple master regulatory trans-eQTLs including the major histocompatibility complex (MHC), coding variants altering enzyme and receptor function, an IFN-ß cytokine network showing temporal specificity, and an interferon regulatory factor 2 (IRF2) transcription factor-modulated network. Induced eQTL are significantly enriched for genome-wide association study loci, identifying context-specific associations to putative causal genes including CARD9, ATM, and IRF8. Thus, applying pathophysiologically relevant immune stimuli assists resolution of functional genetic variants.